//
// ExpansionHunter
// Copyright 2016-2020 Illumina, Inc.
// All rights reserved.
//
// Author: Egor Dolzhenko <edolzhenko@illumina.com>
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//      http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
//

#pragma once

#include <unordered_set>

#include "core/Common.hh"
#include "genotyping/AlignMatrix.hh"
#include "genotyping/RepeatGenotype.hh"

namespace ehunter
{
namespace strgt
{

std::unordered_set<int> getAlleleCandidates(int readLen, int motifLen, const AlignMatrix& alignMatrix);

RepeatGenotype genotype(AlleleCount alleleCount, int motifLen, int readLen, int fragLen, AlignMatrix& alignMatrix);

}
}
